PHB says that masterwork armor never appear expect as a magic object. Reading the descriptions of the masterwork armors, all of them require some sort of magic in the crafting, so I get the point to make them appear only as magic objects.The problem arise when considering armors made of mythical beasts hides or scales (the Dark Sun campaign setting has a few example of those): it doesn't seem to me that magic would be necessary to craft those types of armor, so I'm thinking that it may be possible to include those armors in a non magical fashion.What's your thought on the matter?

PHB says all magic armour is masterwork. PHB does not say that all masterwork armour is magical. That said, the price is such that it will almost never be had by any character under any circumstances, short of a GM giving it as loot. It is simply to expensive for what it actually does.

You can certainly magical non-magical leather armour (or "hide armour") out of such animal skins. You could even make masterwork versions of such armour. It it was made as a masterwork armour, you could then go on to enchant it.

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There is non magical masterwork armor, it gives non magical bonuses. (It has been a few months since playing 4e so forgive me if I am slightly incorrect)I don't remember reading that you needed magic to create the masterwork armor.

Now on to my thoughts on non magical hide armors;I think it could be done to have say a non magical dragon scale armor, but what a waste of resources for a pc.An armorer or supplier would still have to kill a dragon to get it, then have the resulting armor be worth less than +1 magical would be annoying.The masterwork non magical bonuses are not figured in to attack that ignore normal defenses and you may need magical defenses against some attacks.If i had the hide I would not make it non magical, I would quest for whatever it took for the magical version.

final thoughts;It is your campaign so do what you think is best, if it makes sense in your world and it is fun, do it.